Arachne Main Page

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[[Arachne Main Page|ARACHNE]] is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.
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[[Arachne]] is the [[Whole Genome Shotgun]] Assembler developed at the Broad Institute.
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<br style="clear: both" />
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Under continuous development since 2000, the Arachne software package has evolved from the classic "overlap-layout-consensus" paradigm into a vast collection of different tools and modules, some to modify and manipulate assemblies, others to analyze and gather statistics or vizualize genomes. The current version of Arachne can be downloaded as source code.
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== Quick Links ==
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To participate in this wiki, please send mail to [mailto:arachne@broad.mit.edu arachne@broad.mit.edu] to ask for an account.
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=== Arachne Reference ===
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== Downloads ==
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* [[Setup]]
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* [[Input]]
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* [[Running Arachne]]
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* [[Output]]
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* [[Looking at Assemblies]]
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* [[Improving Assemblies]]
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* [[Independent Modules]]
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* [[Installation]]: how to download, install, and compile Arachne.
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=== Downloads ===
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== Using Arachne ==
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* [ftp://ftp.broadinstitute.org/pub/crd/nightly/arachne/ Nightly Build]: The current state of Arachne - updated within the last 24 hours.
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* [ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/sample_projects.tar.gz Sample Projects]: Ready-made examples of Arachne input.
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* [[Input]]: how to set up input files.
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=== Miscellaneous ===
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* [[Running Arachne]]: from traces to the draft genome.
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* [[Output]]: how the output looks like, and how to translate it in a human readable format.
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* [[Analysis]]: how to examine your assembly.
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* [[Restricted:Algorithms|Algorithms]]: you have your first assembly, now you want to make it better. Here, you might find out how.
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== Miscellaneous ==
 
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* [[ArachneWiki:About|About this resource]]: what's in here, why, and how to find it.
 
* Arachne's [[lore]]
* Arachne's [[lore]]
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== External links ==
== External links ==
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* [http://en.wikipedia.org/wiki/DNA_sequencing DNA Sequencing]
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* [[w:Genome assembly|Genome assembly]]
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* [http://en.wikipedia.org/wiki/Shotgun_sequencing Shotgun Sequencing]
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* [[w:Shotgun sequencing|Shotgun sequencing]]
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* [http://www.broadinstitute.org/ Broad Institute]
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== Publications ==
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Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. January, 2002. ''[http://www.ncbi.nlm.nih.gov/pubmed/11779843 ARACHNE: a whole-genome shotgun assembler. Genome Research]'' 12: 177 - 189.
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Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. January, 2003. ''[http://www.ncbi.nlm.nih.gov/pubmed/12529310 Whole-genome sequence assembly for mammalian genomes: Arachne 2]. Genome Research'' 13: 91 - 96.
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Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB: August, 2009.
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''[http://genomebiology.com/2009/10/8/R88 Assisted assembly: how to improve a de novo genome assembly by using related species]. Genome Biology'' 10: R88.

Current revision

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.


Quick Links

Arachne Reference

Downloads

Miscellaneous

External links

Publications

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. January, 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12: 177 - 189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. January, 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Research 13: 91 - 96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB: August, 2009. Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biology 10: R88.

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